Replication - Part 2 Flashcards
(76 cards)
1
Q
- always at the same position on a DNA molecule
- “origin of replication”
A
initiation
2
Q
origin of replication in prokaryotes, viruses
A
oriC
3
Q
how many origin of replications are there in prokaryotes and viruses
A
single origin
4
Q
how many origin of replications are there in eukaryotes
A
multiple
5
Q
no. of replication origin in yeast
A
300 origins
6
Q
no. of replication origin in humans
A
20,000 origins
7
Q
- segment of DNA that replicates from a single origin of replication
- genome is divided into
A
replicons
8
Q
origin of replication in E.coli
A
oriC
9
Q
no. of base pairs in oriC
A
~245 bp
10
Q
two parts of the oriC
A
- 13-nuc repeat motif
- 9-nuc repeat motif
11
Q
- repeated 3x
- consensus seq: 5’GATCTNTTNTTTT3’
A
13-nuc repeat motif
12
Q
how many times is the 13-nuc repeat motif repeated
A
3
13
Q
- repeated 5x
- consensus seq: (di ma type kapoi)
A
9-nuc repeat motif
14
Q
how many times is the 9-nuc repeat motif repeated
A
5
15
Q
what is formed in the 13 nucleotide repeat motif once dnaA is present
A
melted region
16
Q
binds to 9-nuc repeat of oriC
A
DnaA
17
Q
what does the dnaA do
A
tortional stress on DNA
18
Q
what happens at 13-nuc repeat of oriC
A
melting of helix
19
Q
attaches to the melted region
A
dnaBC
20
Q
later detaches
A
dnaC
21
Q
what is formed after dnaC detaches
A
pre-priming complex
22
Q
what does dnaB do
A
unwinds more DNA
23
Q
releases tension during the unwinding of dnaB
A
DNA topoisomerase
24
Q
attaches to ssDNA
A
SSB
25
primase that attaches to DNA
DnaG
26
initial assembly of the complex that initiates primer synthesis
primosome
27
dimer that binds after RNA primer is synthesized
DNA pol III
28
enhances binding of DNA pol III
sliding clamp
29
large protein complex that carries out DNA replication, starting at the replication origin
replisome
30
Detaches SSB once DNA pol III arrrives to copy template
replication mediator protein (RMP)
31
proofreads and replaces primers
DNA pol I
32
seals nicks
DNA ligase
33
what happens after DNA ligase seals nicks
termination of replication
34
replication fork in 3D:
the DNA on the lagging strand is __
folded
35
termination of replication
genetically determined
36
hypotheses of termination of replication
1. secondary structure hinders progress of replication fork
2. terminus destablizes components of replication machinery
3. protein binds terminus and modifies binding or action of replisome
37
hinders progress of replication fork
secondary structure
38
destablizies components at replication machinery
terminus
39
binds terminus and modifies binding or action of replisome
protein
40
- defined termination sequence
- 23bp consensus sequence
- binding site of ter protein which has contra-helicase activity
ter element
41
what binds to ter element
ter protein
42
what does the ter protein have
contra-helicase activity
43
replication models for circular DNA
1. theta model
2. rolling circle model
44
DNA in theta model
1. bacterial DNA
2. λ DNA
45
DNA in rolling circle model
1. F factor
2. ø X 174 DNA
3. λ DNA
46
products of theta replication
two circular DNA molecules
47
where continuous DNA synthesis begin in rolling-circle model
3' end of broken nucleotide strand
48
how is replication initiated in rolling circle model
break in one of nucleotide strands
49
what is released in rolling circle model
1. ss linear DNA
2. ds circular DNA
50
creates a nick in rolling circular model
endonuclease
51
origin of replication for yeast
ARS (autonomously replicating sequence)
52
ARS subdomains
1. A and B1 = ORS
2. B2
3. B3
53
A and B1
ORS
54
function of ORS
binding site of ORC
55
ORC
origin replicating complex
56
ORS
origin replication sequence
57
function of B2
melting
58
function of B3
binding site of ABF
- tortional stress on DNA
59
ABF
ARS binding factor 1 protein
60
- tightly bound
- cooperates in the synthesis of the first few nucleotides of the new polynucleotide
eukaryotic primase and DNA pol α
61
synthesizes an RNA primer
primase
62
no. of nucleotides of RNA in RNA primer
8-12
63
extends the RNA primer by adding ~20 nucs of DNA
DNA pol α
64
how many nucs does DNA pol α add to extend RNA primer
~20 nucs
65
elongates RNA
DNA pol δ
66
how many eukaryotic DNA polymerases are there
10
67
for primer synthesis in eukaryotes
DNA pol α
68
for mitochondrial DNA replication
DNA pol γ
69
main elongating enzyme
DNA pol δ
70
works with DNA pol δ by increasing its processivity
Proliferating cell nuclear antigen (PCNA)
71
removes RNA primers in eukaryotes
RNase H, FEN1
72
accuracy of DNA replication
1. specificity of base pairing
2. pre-synthetic error control
3. proof-reading ability of DNA polymerase
73
before the nucleotide is covalently added to the growing chain
pre-synthetic error control
74
what does DNA pol undergo during pre-synthetic error contrl
conformational change
75
what does the DNA pol do during pre-synthetic error control
double-checks exact base pair geometry
76
DNA repair mechanisms to correct replication errors
proof-reading ability (3'-5' exonuclease)
